Error in TCGAbiolinks TCGAanalyze_Preprocessing

l0o0 commented 7 years ago

I am doing the pipeline according this toturial.

clin = GDCquery_clinic("TCGA-BRCA","clinical")
samples = clin[clin$gender=='female',]
miRNA = GDCquery(project='TCGA-BRCA', data.type='miRNA Expression Quantification',     data.category="Transcriptome Profiling")
GDCdownload(miRNA, method='api')
dataPrep = GDCprepare(query=miRNA)
data1 = TCGAanalyze_Preprocessing(object = dataPrep,cor.cut = 0.6)

At last step, It comes an error:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function assays for signature "data.frame"

I found this issue37 report a similar error.
I try to run the command in that issue:

library(SummarizedExperiment)
assays(dataPrep)

the error is still there. May be some errors in my code ?

ghost commented 5 years ago

Hi, @l0o0

I have same issue now in LGG data.

So if you solved this problem, could you give me reply?

I look forward to hearing you.

Thank you.

l0o0 commented 5 years ago

@diceofeugene This problem was two years ago, I can not remember whether this problem was solved. I am sorry for that.

AnkitaShukla17 commented 5 years ago

If the above said problem get solved please share the procedure.

AnkitaShukla17 commented 5 years ago

The problem get solved. For this in GDCprepare step set summarizedExperiment = TRUE. This is it, you will not face problem in preprocessing step thereafter.

BioinformaticsFMRP / TCGAbiolinks

Error in TCGAbiolinks TCGAanalyze_Preprocessing #107